Variant report

Variant	rs224799
Chromosome Location	chr4:48021925-48021926
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48019513..48022096-chr4:48074921..48077158,2	MCF-7	breast:
2	chr4:48021540..48023440-chr4:48027193..48032829,5	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs13116684	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13121957	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13125949	0.80[AFR][1000 genomes]
rs13140968	0.94[AFR][1000 genomes]
rs13142905	0.80[AFR][1000 genomes]
rs13145218	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13150783	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13151608	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs321622	0.97[AFR][1000 genomes]
rs321628	0.85[AFR][1000 genomes]
rs321630	0.85[AFR][1000 genomes]
rs321631	0.85[AFR][1000 genomes]
rs321632	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs321634	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs321635	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35085584	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695325	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55670663	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447609	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6812991	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7674929	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs98270	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1013947	chr4:47915527-48052824	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537082	chr4:47915527-48052824	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1006745	chr4:47935250-48052824	Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv537083	chr4:47935250-48052824	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1013163	chr4:47977844-48022511	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv537084	chr4:47977844-48022511	Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs224799	CNGA1	cis	Thyroid	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48019800-48022600	Weak transcription	Gastric	stomach
2	chr4:48019800-48022600	Weak transcription	Small Intestine	intestine
3	chr4:48019800-48024200	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr4:48019800-48024400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:48019800-48026000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:48019800-48026600	Weak transcription	NH-A	brain
7	chr4:48019800-48027600	Weak transcription	Placenta	Placenta
8	chr4:48019800-48030200	Weak transcription	Psoas Muscle	Psoas
9	chr4:48019800-48033800	Weak transcription	Pancreas	Pancrea
10	chr4:48019800-48033800	Weak transcription	Hela-S3	cervix
11	chr4:48019800-48034000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr4:48019800-48034200	Weak transcription	HepG2	liver
13	chr4:48019800-48043600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr4:48019800-48049800	Weak transcription	Esophagus	oesophagus
15	chr4:48020000-48026600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:48020000-48029200	Weak transcription	GM12878-XiMat	blood
17	chr4:48020400-48027600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr4:48020600-48022000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:48020600-48022400	Weak transcription	Liver	Liver
20	chr4:48020600-48022800	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr4:48020600-48023000	Enhancers	Duodenum Mucosa	Duodenum
22	chr4:48020600-48026200	Weak transcription	Fetal Heart	heart
23	chr4:48020600-48049600	Weak transcription	Colonic Mucosa	Colon
24	chr4:48020800-48022400	Weak transcription	NHEK	skin
25	chr4:48020800-48024200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:48020800-48025000	Enhancers	Fetal Intestine Small	intestine
27	chr4:48020800-48025400	Enhancers	Fetal Intestine Large	intestine
28	chr4:48020800-48026600	Weak transcription	HMEC	breast
29	chr4:48021000-48026400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr4:48021200-48022200	Active TSS	Rectal Mucosa Donor 29	rectum
31	chr4:48021600-48034200	Weak transcription	Stomach Mucosa	stomach
32	chr4:48021800-48022400	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr4:48021800-48026800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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